That version seems to be meant for use with GAP4.4, which, in as far
as I know, is not out yet:

if IsFinite(G) and CompareVersionNumbers( VERSION, "4.4" ) then
SetIsGroupOfAutomorphismsFiniteGroup(A,true);
fi;

version 1.11 does not have the problem.

My best guess is that the warning is a nuisance, but harmless.
The authors, whom I believe read this site, could confirm or deny this
and maybe do something to suppress the warning in older (that is
already released) versions of GAP.